If you are connecting the CA9100 to the MTII's stereo balanced RCA inputs you are surely experiencing the dreaded "sprinkler noise" that was much discussed here years ago when the MTII was first released and a number of tapers were using them. The sprinkler noise occurs when an unbalanced signal is fed into these inputs.
this.
...........and if possible, find yourself an M10... and never worry again.
The original MT is great for analog input, but can be finicky.
The MT II is great for digital, but can be finicky.
Both are great little decks, but both can be goofy in their own respects.